1. Discussion Section 3 HW1 comments HW2 questions
Maximal D-Segment algorithm
Useful data structures

2. HW1 comments Testing Working together Formatting
Test cases with known output
Built-in checks (e.g. match locations for a string and its reverse complement should have the same position, on opposite strands)
Working together
It’s okay to compare final output, just not code
Formatting
Submit a plain text file (not rtf or Word)
Include your name in the filename

3. HW2 questions?
Notes:
Assume that any input graph text file lists the vertices in depth order
Write your representation of the graph image in depth order
Make sure you write the sequence graph file in depth order
How do you find the vertex at the beginning of the path?

4. Maximal segment vs. Maximal D-segment
No subsegment has a higher score
No segment properly containing the segment satisfies the above condition
Does NOT imply that no supersegment has a higher score
Maximal D-segment:
No subsegment has score < D, where dropoff D < 0
No D-segment properly containing the D-segment satisfies the above condition
The segment score must be >= S, where S >= -D

6. D
cumulative score S
find the maximal d segments
sequence position

7. D
cumulative score S
sequence position

8. D
cumulative score S
sequence position

9. Pseudo-code for the D-segment algorithm:

10. D = -3 S = 3 max = 0 start = 1 end = 1 cumul = 0
position
# read starts
score
D = -3
S = 3
max = 0
start = 1
end = 1
cumul = 0

11. D = -3 S = 3 max = 0 start = 2 end = 2 cumul = 0
position
# read starts
score
D = -3
S = 3
max = 0
start = 2
end = 2
cumul = 0

12. D = -3 S = 3 max = 0 start = 2 end = 2 cumul = 0
position
# read starts
score
D = -3
S = 3
max = 0
start = 2
end = 2
cumul = 0

13. D = -3 S = 3 max = 0 start = 3 end = 3 cumul = 0
position
# read starts
score
D = -3
S = 3
max = 0
start = 3
end = 3
cumul = 0

14. D = -3 S = 3 max = 0 start = 3 end = 3 cumul = 0
position
# read starts
score
D = -3
S = 3
max = 0
start = 3
end = 3
cumul = 0

15. D = -3 S = 3 max = 0 start = 4 end = 4 cumul = 0
position
# read starts
score
D = -3
S = 3
max = 0
start = 4
end = 4
cumul = 0

16. D = -3 S = 3 max = 0 start = 4 end = 4 cumul = 0
position
# read starts
score
D = -3
S = 3
max = 0
start = 4
end = 4
cumul = 0

17. D = -3 S = 3 max = 0 start = 5 end = 5 cumul = 0
position
# read starts
score
D = -3
S = 3
max = 0
start = 5
end = 5
cumul = 0

18. D = -3 S = 3 max = 0 start = 5 end = 5 cumul = 0
position
# read starts
score
D = -3
S = 3
max = 0
start = 5
end = 5
cumul = 0

19. D = -3 S = 3 max = 0.52 start = 5 end = 5 cumul = 0.52
position
# read starts
score
D = -3
S = 3
max = 0.52
start = 5
end = 5
cumul = 0.52

20. D = -3 S = 3 max = 0.52 start = 5 end = 5 cumul = 0.52
position
# read starts
score
D = -3
S = 3
max = 0.52
start = 5
end = 5
cumul = 0.52

21. D = -3 S = 3 max = 1.62 start = 5 end = 6 cumul = 1.62
position
# read starts
score
D = -3
S = 3
max = 1.62
start = 5
end = 6
cumul = 1.62

22. D = -3 S = 3 max = 1.62 start = 5 end = 6 cumul = 1.62
position
# read starts
score
D = -3
S = 3
max = 1.62
start = 5
end = 6
cumul = 1.62

23. D = -3 S = 3 max = 1.62 start = 5 end = 6 cumul = 1.12
position
# read starts
score
D = -3
S = 3
max = 1.62
start = 5
end = 6
cumul = 1.12

24. D = -3 S = 3 max = 1.62 start = 5 end = 6 cumul = 1.12
position
# read starts
score
D = -3
S = 3
max = 1.62
start = 5
end = 6
cumul = 1.12

25. D = -3 S = 3 max = 2.82 start = 5 end = 8 cumul = 2.82
position
# read starts
score
D = -3
S = 3
max = 2.82
start = 5
end = 8
cumul = 2.82

26. D = -3 S = 3 max = 2.82 start = 5 end = 8 cumul = 2.82
position
# read starts
score
D = -3
S = 3
max = 2.82
start = 5
end = 8
cumul = 2.82

27. D = -3 S = 3 max = 3.34 start = 5 end = 9 cumul = 3.34
position
# read starts
score
D = -3
S = 3
max = 3.34
start = 5
end = 9
cumul = 3.34

28. D = -3 S = 3 max = 3.34 start = 5 end = 9 cumul = 3.34
position
# read starts
score
D = -3
S = 3
max = 3.34
start = 5
end = 9
cumul = 3.34

29. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 4.44
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 4.44

30. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 4.44
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 4.44

31. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 3.94
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 3.94

32. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 3.94
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 3.94

33. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 3.44
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 3.44

34. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 3.44
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 3.44

35. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 2.94
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 2.94

36. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 2.94
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 2.94

37. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 2.44
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 2.44

38. D = -3 S = 3 max = 4.44 start = 5 end = 10 cumul = 2.44
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 2.44

39. D-segment: 5, 10, 4.44 (start, end, max)
position
# read starts
score
D = -3
S = 3
max = 4.44
start = 5
end = 10
cumul = 2.44
D-segment: , 10, (start, end, max)

40. HW3 Due 11:59pm on Sunday, January 28
Assignment: use D-segment algorithm to identify sequence segments with high copy number.
Input:
Count file reporting number of read starts at each location
Scoring scheme
Output:
Number of normal and elevated copy-number segments
List of elevated copy-number segments (start, end, score)
Annotations for the first three segments (look up using UCSC genome browser)
Histograms of read-start counts (i.e. number of positions with 0, 1, 2, and >=3 read-starts) for non-elevated and elevated segments

41. Useful data structures
Arrays
Fast indexing, pointer math is easy
Linked lists
Inserting/deleting/reordering is easy
Hash tables/maps
Good for looking up things
Trees
Useful for sorting/searching
More on pros/cons of different data structures, and the runtimes of typical operations here.